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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 4-76325890-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=76325890&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CCDC158",
"hgnc_id": 26374,
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_001394954.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 4,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0749,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.64,
"chr": "4",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.04220786690711975,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3778,
"cdna_start": 3429,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "NM_001394954.1",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000682701.1",
"protein_coding": true,
"protein_id": "NP_001381883.1",
"strand": false,
"transcript": "NM_001394954.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3778,
"cdna_start": 3429,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000682701.1",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001394954.1",
"protein_coding": true,
"protein_id": "ENSP00000507278.1",
"strand": false,
"transcript": "ENST00000682701.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3393,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000504667.2",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "n.3002G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000504667.2",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1113,
"aa_ref": "A",
"aa_start": 1042,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3626,
"cdna_start": 3277,
"cds_end": null,
"cds_length": 3342,
"cds_start": 3124,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "NM_001042784.1",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3124G>C",
"hgvs_p": "p.Ala1042Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001036249.1",
"strand": false,
"transcript": "NM_001042784.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1113,
"aa_ref": "A",
"aa_start": 1042,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3663,
"cdna_start": 3277,
"cds_end": null,
"cds_length": 3342,
"cds_start": 3124,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "ENST00000388914.7",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3124G>C",
"hgvs_p": "p.Ala1042Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000373566.2",
"strand": false,
"transcript": "ENST00000388914.7",
"transcript_support_level": 5
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3882,
"cdna_start": 3533,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_011531908.3",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530210.1",
"strand": false,
"transcript": "XM_011531908.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3827,
"cdna_start": 3478,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_011531909.3",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530211.1",
"strand": false,
"transcript": "XM_011531909.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4568,
"cdna_start": 4219,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_011531910.4",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530212.1",
"strand": false,
"transcript": "XM_011531910.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3730,
"cdna_start": 3381,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_011531911.2",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530213.1",
"strand": false,
"transcript": "XM_011531911.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3624,
"cdna_start": 3275,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_011531912.3",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530214.1",
"strand": false,
"transcript": "XM_011531912.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3653,
"cdna_start": 3304,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011531913.1",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530215.1",
"strand": false,
"transcript": "XM_011531913.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3735,
"cdna_start": 3386,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011531914.3",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530216.1",
"strand": false,
"transcript": "XM_011531914.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1117,
"aa_ref": "A",
"aa_start": 1046,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4392,
"cdna_start": 4043,
"cds_end": null,
"cds_length": 3354,
"cds_start": 3136,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_017008160.2",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3136G>C",
"hgvs_p": "p.Ala1046Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016863649.1",
"strand": false,
"transcript": "XM_017008160.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1113,
"aa_ref": "A",
"aa_start": 1042,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3766,
"cdna_start": 3417,
"cds_end": null,
"cds_length": 3342,
"cds_start": 3124,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_005262974.5",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.3124G>C",
"hgvs_p": "p.Ala1042Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005263031.1",
"strand": false,
"transcript": "XM_005262974.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1066,
"aa_ref": "A",
"aa_start": 995,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3625,
"cdna_start": 3276,
"cds_end": null,
"cds_length": 3201,
"cds_start": 2983,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 22,
"exon_rank_end": null,
"feature": "XM_011531915.3",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.2983G>C",
"hgvs_p": "p.Ala995Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530217.1",
"strand": false,
"transcript": "XM_011531915.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1035,
"aa_ref": "A",
"aa_start": 964,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3609,
"cdna_start": 3260,
"cds_end": null,
"cds_length": 3108,
"cds_start": 2890,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "XM_011531917.2",
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"hgvs_c": "c.2890G>C",
"hgvs_p": "p.Ala964Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530219.1",
"strand": false,
"transcript": "XM_011531917.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs762178999",
"effect": "missense_variant",
"frequency_reference_population": 0.0000024822211,
"gene_hgnc_id": 26374,
"gene_symbol": "CCDC158",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000205572,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657402,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.438,
"pos": 76325890,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.013,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.15000000596046448,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.15,
"transcript": "NM_001394954.1"
}
]
}